After the signing of the Federation Charter on May 8, 2161, it could be assumed that the United Earth Starfleet Command was either dissolved, absorbed into, or became the Federation incarnation of Starfleet Command that regulates the Federation Starfleet.

After Captain Sisko contacted Starfleet Command about Section 31, Starfleet Command did not acknowledge its existence, but did not deny it, either. Sisko was informed by Starfleet Command that they would look into it. The Starfleet Command investigation into Section 31 was later shelved. (DS9: "Inquisition", "Inter Arma Enim Silent Leges")

The terms "Starfleet" and "Starfleet Command" were first used in TOS: "Court Martial". Prior to this, in terms of air date, those names debuted in "The Menagerie, Part I", though the terms "Star Service" and "Spacefleet Command" were later used in "The Conscience of the King" and "The Squire of Gothos" respectively, prior to the initial airing of "Court Martial". Another early variant of the organization's name was "Space Central" in "Miri", which preceded all those episodes in both airing and production order. In the final draft script of "Court Martial", the organization was instead named "Galactic Command".